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Magnesium in PDB 6fw3: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007, PDB code: 6fw3 was solved by A.K.Singh, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.23 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.110, 110.717, 161.490, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.4

Other elements in 6fw3:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007 (pdb code 6fw3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007, PDB code: 6fw3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6fw3

Go back to Magnesium Binding Sites List in 6fw3
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:13.0
occ:1.00
 OD1 A:ASP201 2.1 15.5 1.0
O A:HOH714 2.1 15.7 1.0
O A:HOH664 2.1 15.9 1.0
O A:HOH617 2.2 16.0 1.0
O A:HOH779 2.2 19.1 1.0
O A:HOH685 2.2 17.4 1.0
CG A:ASP201 3.1 15.4 1.0
OD2 A:ASP201 3.5 15.7 1.0
ZN A:ZN501 3.9 20.5 1.0
OE2 A:GLU230 4.0 20.5 1.0
NE2 A:HIS233 4.0 14.2 1.0
CD2 A:HIS200 4.1 16.9 1.0
O A:HIS200 4.1 15.1 1.0
O A:HOH715 4.2 21.4 1.0
OG1 A:THR271 4.2 17.1 1.0
CD2 A:HIS233 4.3 14.8 1.0
O A:HOH769 4.3 18.6 1.0
CB A:ASP201 4.5 15.8 1.0
C24 A:E8H523 4.5 23.2 1.0
NE2 A:HIS200 4.5 16.8 1.0
CD2 A:HIS204 4.6 19.1 1.0
OD2 A:ASP318 4.6 21.8 1.0
O A:HOH671 4.6 27.7 1.0
O A:THR271 4.7 21.1 1.0
CG A:GLU230 4.7 17.6 1.0
C23 A:E8H523 4.8 24.6 1.0
CA A:ASP201 4.8 15.8 1.0
NE2 A:HIS204 4.8 18.1 1.0
CB A:THR271 4.8 19.4 1.0
CD A:GLU230 4.8 19.6 1.0
C A:HIS200 4.9 15.8 1.0
NE2 A:HIS160 4.9 20.7 1.0
CD2 A:HIS160 5.0 20.7 1.0

Magnesium binding site 2 out of 4 in 6fw3

Go back to Magnesium Binding Sites List in 6fw3
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:13.8
occ:1.00
 OD1 B:ASP201 2.1 19.3 1.0
O B:HOH626 2.1 17.7 1.0
O B:HOH634 2.1 16.9 1.0
O B:HOH745 2.1 17.1 1.0
O B:HOH610 2.2 17.4 1.0
O B:HOH735 2.2 15.6 1.0
CG B:ASP201 3.1 17.9 1.0
OD2 B:ASP201 3.5 16.4 1.0
ZN B:ZN501 3.9 22.5 1.0
OE2 B:GLU230 3.9 21.1 1.0
O B:HIS200 4.1 17.0 1.0
O B:HOH711 4.2 17.6 1.0
NE2 B:HIS233 4.2 18.3 1.0
O B:HOH771 4.2 16.3 1.0
CD2 B:HIS200 4.2 17.7 1.0
OG1 B:THR271 4.2 22.5 1.0
CD2 B:HIS233 4.3 19.5 1.0
O B:THR271 4.4 21.3 1.0
CB B:ASP201 4.4 17.7 1.0
C24 B:E8H517 4.5 22.1 1.0
OD2 B:ASP318 4.5 19.4 1.0
CD2 B:HIS204 4.6 16.8 1.0
NE2 B:HIS200 4.6 17.0 1.0
C23 B:E8H517 4.6 21.7 1.0
O B:HOH642 4.7 21.5 1.0
NE2 B:HIS160 4.7 20.4 1.0
CB B:THR271 4.7 21.1 1.0
CA B:ASP201 4.8 18.4 1.0
NE2 B:HIS204 4.8 16.7 1.0
CG B:GLU230 4.8 18.4 1.0
CD B:GLU230 4.8 19.3 1.0
CD2 B:HIS160 4.8 19.4 1.0
C B:HIS200 5.0 17.1 1.0

Magnesium binding site 3 out of 4 in 6fw3

Go back to Magnesium Binding Sites List in 6fw3
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg504

b:14.1
occ:1.00
 O C:HOH687 2.1 14.8 1.0
OD1 C:ASP201 2.1 18.1 1.0
O C:HOH723 2.1 16.1 1.0
O C:HOH621 2.1 18.7 1.0
O C:HOH711 2.2 15.0 1.0
O C:HOH617 2.2 18.6 1.0
CG C:ASP201 3.1 17.0 1.0
OD2 C:ASP201 3.5 16.7 1.0
ZN C:ZN503 3.9 23.3 1.0
O C:HIS200 4.1 16.3 1.0
OE2 C:GLU230 4.1 20.4 1.0
CD2 C:HIS200 4.1 16.4 1.0
O C:HOH730 4.2 18.4 1.0
O C:HOH693 4.2 19.4 1.0
OG1 C:THR271 4.2 17.9 1.0
NE2 C:HIS233 4.3 15.8 1.0
CD2 C:HIS233 4.3 15.4 1.0
O C:THR271 4.5 20.2 1.0
CB C:ASP201 4.5 16.3 1.0
C24 C:E8H518 4.5 24.5 1.0
OD2 C:ASP318 4.6 21.0 1.0
CD2 C:HIS204 4.6 15.5 1.0
NE2 C:HIS200 4.6 18.2 1.0
CB C:THR271 4.7 20.4 1.0
O C:HOH667 4.7 20.7 1.0
NE2 C:HIS160 4.8 19.5 1.0
C23 C:E8H518 4.8 24.3 1.0
CG C:GLU230 4.8 18.3 1.0
NE2 C:HIS204 4.8 15.6 1.0
CD2 C:HIS160 4.8 18.8 1.0
CA C:ASP201 4.9 18.1 1.0
CD C:GLU230 4.9 19.3 1.0
C C:HIS200 5.0 16.4 1.0

Magnesium binding site 4 out of 4 in 6fw3

Go back to Magnesium Binding Sites List in 6fw3
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-007 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg504

b:11.7
occ:1.00
 OD1 D:ASP201 2.1 16.3 1.0
O D:HOH657 2.1 14.6 1.0
O D:HOH788 2.1 18.6 1.0
O D:HOH709 2.2 14.2 1.0
O D:HOH610 2.2 14.2 1.0
O D:HOH666 2.2 13.0 1.0
CG D:ASP201 3.1 17.5 1.0
OD2 D:ASP201 3.5 16.0 1.0
ZN D:ZN503 3.9 19.4 1.0
OE2 D:GLU230 4.0 20.0 1.0
NE2 D:HIS233 4.1 14.0 1.0
O D:HOH734 4.1 19.0 1.0
O D:HOH782 4.1 19.1 1.0
CD2 D:HIS200 4.2 14.2 1.0
O D:HIS200 4.2 15.1 1.0
OG1 D:THR271 4.2 17.4 1.0
CD2 D:HIS233 4.4 13.8 1.0
C24 D:E8H518 4.4 20.9 1.0
OD2 D:ASP318 4.5 19.3 1.0
CB D:ASP201 4.5 16.3 1.0
NE2 D:HIS200 4.6 15.2 1.0
C23 D:E8H518 4.6 20.1 1.0
O D:THR271 4.6 18.8 1.0
CD2 D:HIS204 4.6 17.3 1.0
CG D:GLU230 4.7 16.5 1.0
O D:HOH684 4.7 23.4 1.0
NE2 D:HIS160 4.8 21.0 1.0
CB D:THR271 4.8 19.3 1.0
CD D:GLU230 4.8 19.8 1.0
CA D:ASP201 4.8 15.8 1.0
CD2 D:HIS160 4.9 20.2 1.0
NE2 D:HIS204 4.9 16.9 1.0
C D:HIS200 5.0 16.1 1.0

Reference:

I.G.Salado, C.Moreno, G.Sakaine, A.K.Singh, A.R.Blaazer, M.Siderius, A.Matheeussen, S.Gul, L.Maes, R.Leurs, D.G.Brown, K.Augustyns. HPDE4D2 Structure with Inhibitor Npd-007 To Be Published.
Page generated: Tue Oct 1 00:53:02 2024

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